Tifa was worried for Cloud's mental state from the moment she found him next to the train in the Sector 7 Slums before the first mission. He was already getting the number of years since they'd seen eachother wrong (actually he was right but yeah, she didn't know that obviously) and a few times throughout the adventure she almost broached the subject with him only to turn wayward. Yeah, it's a weakness on her part. But that's how it goes.
Cloud was drenched in Mako like crazy after he and Zack were taken by Shinra. Before that he didn't have those eyes; he's remembering badly and only Zack did.
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"Setsuna, you have to change. To make up for me... who didn't change." ~SCP~
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